INTEGRATION OF NOVEL SSR MARKERS INTO THE LENTIL (Lens culinaris Medik.) GENOME

Year 2024, , 40 - 45, 21.06.2024

Brian Wakimwayi Koboyi Melike Bakır

https://doi.org/10.17557/tjfc.1415823

Abstract

The development of Simple Sequence Repeat markers (SSRs) for lentil has played a pivotal role in enhancing the comprehension of the lentil genome through genetic mapping. The study aimed to determine the relative positions of newly developed microsatellites to the lentil genome using an F7-derived Recombinant Inbred Lines population (RIL) of 71 individuals developed from a cross between Eston and PI320937. Molecular analysis was performed with 100 newly developed lentil SSR markers and a linkage map was constructed using MapMaker/EXP 3.0b and MapChart 2.2 software. Among the 100 SSR markers, 12 markers exhibited polymorphism, 54 markers were identified as monomorphic, and 34 markers remained unamplified. While 10 out of the 12 polymorphic markers successfully integrated into two linkage groups, covering a cumulative length of 19.2cM, two markers remained unlinked. Linkage group-1, comprised of 8 markers, spanned 4.8cM, and linkage group-2 extended over a length of 14.4cM with two markers. Despite only partially representing 2 out of the 7 chromosomes in the lentil genome, this map holds promise for future mapping studies. Through the addition of markers, it could facilitate marker-assisted selection and the identification of QTLs associated with specific agronomic traits.

Keywords

Linkage map, Microsatellites, Polymorphism, Recombinant Inbred Lines, Segregation Distortion

Ethical Statement

The authors declare no conflict of interest.

Project Number

FCD-2021-10106

Thanks

The authors gratefully acknowledge the financial support from the Erciyes University Scientific Research Unit (Project No: FCD-2021-10106). We are also thankful to Erciyes University Faculty of Agriculture and the Genome and Stem Cell Centre (Genkök) for availing laboratory equipment to enable the smooth implementation of this research.

References

• Andeden, E.E., F.S. Baloch, E. Cakir, F. Toklu, H. Ozkan. 2015. Development, characterization and mapping of microsatellite markers for lentil (Lens culinaris Medik.). Plant Breeding, 134: 589- 598.
• Asp, T., U.K. Frei, T. Didion, K.K. Nielsen, T. Lubberstedt. 2007. Frequency, type, and distribution of EST-SSRs from three genotypes of Lolium perenne, and their conservation across orthologous sequences of Festuca arundinacea, Brachypodium distachyon, and Oryza sativa. BMC Plant Biology. 7: 1-12.
• Ates, D., S. Aldemir, A. Alsaleh, S. Erdogmus, S. Nemli, A. Kahriman, and B. Tanyolac. 2018. A consensus linkage map of lentil based on DArT markers from three RIL mapping populations. Plos One. 13(1), e0191375.
• Ates, D., T. Sever, S. Aldemir, B. Yagmur, H.Y. Temel, H.B. Kaya, B. Tanyolac. 2016. Identification of QTLs controlling genes for Se uptake in lentil seeds. Plos One, 11(3), e0149210.
• Ates, D. 2019. Genetic Diversity In Lentil Landraces Revealed By Diversity Array Technology (DArT). Turkish Journal of Field Crops, 24:252-260
• Avise, J.C. 2012. Molecular markers, natural history, and evolution: Sinnauer Kluwer Academic Publishers. Bakir, M. and A. Kahraman. 2019. Development of new SSR (Simple Sequence Repeat) Markers for Lentils (Lens culinaris Medik.) from genomic library enriched with AG and AC microsatellites. Biochemical Genetic. 57: 338-353.
• Bakir, M., S. Demir, C. Yildirim, and A. Kahraman. 2024. Genomic SSR marker development in lentil (Lens culinaris Medik.) and assessment of cross-species/genera transferability to related legumes. Czech Journal of Genetics and Plant Breeding. 60: 42-49.
• Begna, T. and H. Yesuf . 2021. Genetic mapping in crop plants. Open Journal of Plant Science. 6: 019-026.
• Bett, K.E. and D.R. Cook. 2016. KnowPulse. https://knowpulse.usask.ca/. (Accessed on July 01, 2021).
• Bhadauria, V., L. Ramsay, K.E. Bett, and S. Banniza. 2017. QTL mapping reveals genetic determinants of fungal disease resistance in the wild lentil species Lens ervoides. Scientific Reports. 7:1– 9.
• Biswas, M. K., M.N.R. Baig, Y.J. Cheng, and X.X. Deng. 2010. Retro-transposon based genetic similarity within the genus Citrus and its relatives. Genetic Resources and Crop Evolution. 57: 963-972.
• Demir, S. And M. Bakir. 2022. Development of new SSR markers in lentil by scanning AG and AC enriched libraries with TG and TC repeats. European Journal of Science and Technology. 41: 54-58.
• Devos, P. 1998. Nutritional value of lentils and chickpeas and changes during processing. Lentils for Everyone Symposium. pp. 29-30.
• Dikshit, H.K., A. Singh, D. Singh, M. Aski, N. Jain, V.S. Hegde, A.K. Basandrai, D. Basandrai, T.R. Sharma. 2016. Tagging and mapping of SSR marker for rust resistance gene in lentil (Lens culinaris Medikus subsp. culinaris). Indian J Exp Biol. 54:394-9.
• Duran, Y., R. Fratini, P. Garcia,M. Perez De La Vega. 2004. An intersubspecific genetic map of Lens. Theoretical and Applied Genetics. 108: 1265-1273.
• Eujayl, I., M. Baum, W. Erskine, E. Pehu, and F.J. Muehlbauer. 1997. The use of RAPD markers for lentil genetic mapping and the evaluation of distorted F2 segregation. Euphytica, 96. 405-412.
• Eujayl, I., M. Baum, W. Powell, W. Erskine, E. Pehu. 1998. A genetic linkage map of lentil (Lens sp.) based on RAPD and AFLP markers using recombinant inbred lines. Theoretical and Applied Genetics. 97: 83-89.
• FAOSTAT, 2022. Food and Agriculture Organization of the United Nations statistical database. http://www.fao.org/faostat/en/#data. (Accessed January 22, 2022).
• Ferreira, A., M.F.D. Silva, C.D. Cruz. 2006. Estimating the effects of population size and type on the accuracy of genetic maps. Genetics and Molecular Biology. 29: 187-192.
• Gupta, M., B. Verma, N. Kumar, R.K. Chahota, R. Rathour, S.K. Sharma, T.R. Sharma. 2012. Construction of intersubspecific molecular genetic map of lentil based on ISSR, RAPD and SSR markers. Journal of Genetics. 91: 279–87.
• Gupta, S., H.K. Dikshit, G.P. Mishra, and M. Aski. 2023. Association mapping of total flavonoid content and antioxidant capacities in lentil (Lens culinaris Medik.). Indian Journal of Genetics and Plant Breeding. 83: 326-334.
• Hamwieh, A., S.M. Udupa, W. Choumane, A. Sarker, F. Dreyer, C. Jung, and M. Baum. 2005. A genetic linkage map of Lens sp. based on microsatellite and AFLP markers and the localization of fusarium vascular wilt resistance. Theoretical and Applied Genetics. 110: 669-677.
• Havey, M.J. andF.J. Muehlbauer F.J. 1989. Linkages between restriction fragment length, isozyme and morphological markers in Lentil. Theoretical and Applied Genetics. 77: 395- 401.
• Jain, S.K., E.J.V. Wettberg, S.S. Punia, A.K. Parihar, A. Lamichaney, J. Kumar, D.S. Gupta, S. Ahmad, N.C. Pant, G.P. Dixit, et al. 2023. Genomic-mediated breeding strategies for global warming in chickpeas (Cicer arietinum L.). Agriculture. 13(9), 1721.
• Jha, R., A. Bohra, U.C. Jha, M. Rana, R.K. Chahota, S. Kumar, and T.R. Sharma. 2017. Analysis of an intraspecific RIL population uncovers genomic segments harbouring multiple QTL for seed relevant traits in lentil (Lens culinaris L.). Physiology and Molecular Biology of Plants. 23: 675-684.
• Kahraman, A., U.A. Yildirim, and M. Bakir. 2019. Using SSR markers in lentil genome mapping. Journal of Adyutayam. 7: 14-22.
• Kirungu, J. N., R.O. Magwanga, M.L. Shiraku, P. Lu, T.G. Mehari, Y. Xu, and F. Liu. 2020. Genetic map construction and functional characterization of genes within the segregation distortion regions (SDRs) in the F2: 3 populations derived from wild cotton species of the D genome. Journal of Cotton Research. 3: 1-19.
• Kosambi, D.D. 2016. The estimation of map distances from recombination values. In DD Kosambi (pp. 125-130). Springer, New Delhi.
• Koyama, M.L., A. Levesley, R.M. Koebner, T.J. Flowers, A.R. Yeo. 2001. Quantitative trait loci for component physiological traits determining salt tolerance in rice. Plant Physiology. 125: 406-422.
• Kumar, J., S. Gupta, D.S. Gupta, and N.P. Singh. 2018. Identification of QTLs for agronomic traits using association mapping in lentil. Euphytica. 214: 1-15.
• Lander, E.S., P. Green, J. Abrahamson, A. Barlow, M.J. Daly, S.E. Lincoln, L. Newburg. 1987. Mapmaker: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics. 1: 174-181.
• Lefort, F., M. Lally, D. Thompson, G.C. Douglas. 1998. Morphological traits, microsatellite fingerprinting and genetic relatedness of a stand of elite oaks (Q. robur L.) at Tullynally, Ireland. Silvae Genetica. 47: 257-261.
• Paterson, A. H., J.E. Bowers, M.D. Burow, X. Draye, C.G. Elsik, C.X. Jiang, and R.J. Wright. 2000. Comparative genomics of plant chromosomes. The Plant Cell. 12: 1523-1539.
• Phan, H. T., S.R. Ellwood, J.K. Hane, R. Ford, M. Materne, and r.p. Oliver. 2007. Extensive macrosynteny between Medicago truncatula and Lens culinaris ssp. culinaris. Theoretical and Applied Genetics. 114: 549-558.
• Podder, R. 2012. The potential for breeding for stemphylium blight resistance in the genus Lens Master of Science (M. Sc.), University of Saskatchewan.
• Pootakham, W., P. Ruang-Areerate, N. Jomchai, C. Sonthirod, D. Sangsrakru, T. Yoocha. 2015. Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS). Front. Plant Sci. 6:367.
• Qureshi, M.I., S. Muneer, H. Bashir, J. Ahmad, M. Iqbal. 2010. Nodule physiology and proteomics of stressed legumes. In Advances in Botanical Research. 56: 1-48. Academic Press.
• Radhika, P., S.J.M. Gowda, N.Y. Kadoo, L.B. Mhase, B.M. Jamadagni, M.N. Sainani, V.S. Gupta. 2007. Development of an integrated intraspecific map of chickpea (Cicer arietinum L.) using two recombinant inbred line populations. Theoretical and Applied Genetics. 115: 209-216.
• Rajesh, P.N., D. White, G. Saha, W. Chen, F. Muehlbauer. 2008. Development and genetic analysis of SSR markers in lentil. Plant &Animal Genomes XVI Conference, January 12-16, Town & Country Convention Center, San Diego, CA.
• Rubeena, F.R. and P.W.J. Taylor. 2003. Construction of an intraspecific linkage map of lentil (Lens culinaris ssp. culinaris). Theoretical and Applied Genetics. 107: 910-916.
• Saha, G. C., A. Sarker, W. Chen, G.J. Vandemark, and F.J. Muehlbauer. 2010. Inheritance and linkage map positions of genes conferring resistance to stemphylium blight in lentil. Crop Sci. 50: 1831– 1839.
• Saha, G.C., A. Sarker, W. Chen, G.J. Vandemark, F.J. Muehlbauer. 2013. Inheritance and Linkage Map Positions of Genes Conferring Agromorphological Traits in Lens culinaris Medik. International Journal of Agronomy.
• Sari D., Sari H., Ikten C. et al. 2023. Genome-wide discovery of di-nucleotide SSR markers based on whole genome resequencing data of Cicer arietinum L. and Cicer reticulatum Ladiz. Sci Rep. 13, 10351.
• Schuelke, M. 2000. An economic method for the fuorescent labelling of PCR fragments. Nat Biotechnol. 18:233–234
• Septiningsih, E.M., D.L. Sanchez, N. Singh, P. Sendon, A.M. Pamplona, S. Heuer, D.J. Mackill. 2012. Identifying novel QTLs for submergence tolerance in rice cultivars IR72 and Madabaru. Theoretical and Applied Genetics. 124: 867-874.
• Singh, A., H.K. Dikshit, G.P. Mishra, M. Aski, and S. Kumar. 2019. Association mapping for grain diameter and weight in lentil using SSR markers. Plant Gene. 20, 100204.
• Singh, J., A. Sirari, H. Singh, A. Kumar, M. Jaidka, K.S. Mandahal, and S. Singh. 2021. Identifying and validating SSR markers linked with rust resistance in lentil (Lens culinaris). Plant Breeding, 140: 477-485.
• Sonante, G. and D. Pignone. 2001. Assessment of genetic variation in a collection of lentil using molecular tools. Euphytica. 120: 301– 307.
• Sudheesh, S., P. Verma, J.W. Forster, N.O. Cogan, and S. Kaur. 2016. Generation and characterisation of a reference transcriptome for lentil (Lens culinaris Medik.). International Journal of Molecular Sciences, 17(11), 1887.
• Tadmor, Y., D. Zamir, G. Ladizinsky. 1987. Genetic mapping of an ancient translocation in the genus Lens. Theoretical and Applied Genetics. 73: 883-892.
• Tahir, M. and F.J. Muehlbauer. 1994. Gene mapping in lentil with recombinant lines. J. Hered. 85: 306–310.
• Takumi, S., Y. Motomura, J.C.M. Iehisa, et al. 2013. Segregation distortion caused by weak hybrid necrosis in recombinant inbred lines of common wheat. Genetica. 141: 463–70.
• Tanksley, S.D., M.W. Ganal, J.P. Prince, M.C. De Vicente, M.W. Bonierbale, P. Broun, G. Martin. 1992. High density molecular linkage maps of the tomato and potato genomes. Genetics, 132: 1141-1160.
• Tanyolac, B., S. Ozatay, A. Kahraman, F. Muehlbauer. 2010. Linkage mapping of lentil (Lens culinaris L.) genome using recombinant inbred lines revealed by AFLP, ISSR, RAPD and some morphologic markers. J Agric Biotechnol Sustain Dev. 2: 001—006
• Temel, H. Y., D. Gol, A. Kahriman, and M.B. Tanyolac. 2014. Construction of linkage map through genotyping-bysequencing in lentil. In proceedings of Plant and Animal Genome Conference. (Vol. 22, p.358).
• Topu, M., U. Sesiz, H. Bektas, F. Toklu, and H. Ozkan. 2023. Next-generation-sequencing-based simple sequence repeat (SSR) marker development and linkage mapping in lentil (Lens culinaris L.). Life. 13(7), 1579.
• Tullu, A., L. Buchwaldt, T. Warkentin, et al., 2003. Genetics of resistance to anthracnose and identification of AFLP and RAPD markers linked to the resistance gene in PI 320937 germplasm of lentil (Lens culinaris Medikus). Theor Appl Genet. 106: 428–434.
• Tullu, A., B. Tar'an, C. Breitkreutz, S. Banniza, T.D. Warkentin, A. Vandenberg, and L. Buchwaldt, L. 2006. A quantitativetrait locus for resistance to ascochyta blight [Ascochyta lentis] maps close to a gene for resistance to anthracnose [Colletotrichum truncatum] in lentil. Canadian journal of plant pathology. 28: 588-595.
• Tullu, A., B. Tar'an, T. Warkentin, A. Vandenberg. 2008. Construction of an intraspecific linkage map and QTL analysis for earliness and plant height in lentil. Crop Science. 48: 2254-2264.
• Vaillancourt, R. E. and A.E. Slinkard. 1993. Inheritance of new genetic markers in lentil (Lens Miller). Euphytica 42: 227– 236. Verma, P., R. Goyal, R. Chahota, T.R. Sharma, M. Abdin, S. Bhatia. 2015. Construction of a Genetic Linkage Map and Identification of QTLs for Seed Weight and Seed Size Traits in Lentil (Lens culinaris Medik.). Plos One.10:(10).
• Vieira M.L.C., L.Santini, A.L. Diniz and C.D.F. Munhoz. 2016. Microsatellite markers: what they mean and why they are so useful. Genetics and Molecular Biology. 39: 312-328.
• Voorrips, R. 2002. MapChart: software for the graphical presentation of linkage maps and QTLs. Journal of Heredity. 93: 77-78.
• Zamir, D. and G. Ladizinsky. 1984. Genetics of allozyme variants and linkage groups in lentil. Euphytica. 33: 329–336.